Genetics, Bioinformatics and Systems Biology Colloquium
Thursdays, 12:00 pm – 1:00 pm
UC San Diego, Powell-Focht Bioengineering Hall, Fung Auditorium
Complete schedule here

Cytoscape Clinic 2016

Wednesday, Sep 7, 2016 from 9:00 am – 1 pm

UC San Diego Campus, BRF2 room 1102

Organized by Barry Demchak

In this workshop, the Cytoscape development team will try something completely new.

Attendees at our yearly Spring workshop have requested a non-lecture format where individuals can pose problems that will be directly addressed by Cytoscape tutors and developers. This Fall workshop will be like a clinic, where a Cytoscape user signs up for a 15 minute slot where he/she can present a problem (hopefully with actual data), and Cytoscape tutors, developers, and users address it directly on the spot. Anyone interested in hearing the presentation and profiting from the discussion and solution is welcome to attend.
We can assist walk-ins as resources permit, though we strongly recommend signing up for a slot so the Cytoscape team can be best prepared to give good answers.


Please visit here to register.



Note: The schedule will be updated as time slots are assigned

9:30 am Introduction / Installing Cytoscape
10:15 am Learning how to look at mass spec data in Cytoscape
10:30 am How do you choose a suitable input file format?
What are the trade-offs?
Can layouts be described separately from content?
10:45 am How should one select between layout formats?
11:00 am How to build models from which metabolic networks arise
11:15 am  Your questions, answered (please select a time slot here)
11:30 am  Your questions, answered (please select a time slot here)
11:45 am  Your questions, answered (please select a time slot here)
12:00 pm  Your questions, answered (please select a time slot here)
12:15 pm  Your questions, answered (please select a time slot here)
12:30 pm  Your questions, answered (please select a time slot here)



Bring a PC/Mac if possible. No preparation is necessary for the Startup slots, but for subsequent slots, we strongly recommend that attendees have a working Cytoscape installation on their workstations.


No Show Policy

While we do not charge a fee to attend this event, these and our other events would be unsustainable unless those unable to attend cancelled their reservations no later than 2 days before the event. A no-show can limit your ability to book our events in the future. Thank you in advance for your cooperation.



Parking at UC San Diego’s School of Medicine is available to all faculty, staff, and visitors. The closest parking lots are P602, P603, and the Gilman Parking structure. A map of BRF2 and the parking lots and can be seen here. Hourly rates are posted at meters; cards are accepted. If using the UC San Diego Shuttle, exit at Gilman and Meyers and walk south towards School of Medicine.


With additional support provided by Flu-OMICS

Flu-OMICS is funded by a grant from the NIH/NIAID U19AI106754